Color by atom type from a script

Assign color by B-factor

Representation-independent color control

Bonds

PyMOL can deduce bonds from the PDB structure file, even if the CONECT records are missing. In fact, PyMOL guesses bonding connectivity based on proximity, based on the empirical observation that two atoms of a given radius will not be generally closer than a certain distance unless they are bonded.

Displaying double bonds

A higher value for valence spreads things out more. See the Valence page for more information on options for changing the appearance of the valence lines.

Hydrogen bonds and Polar Contacts

Polar Contacts in PyMol

Using the actions [A] button for an object or selection you can display Hydrogen bonds and Polar Contacts.
[A]->find->polar contacts-><select from menu>

The command behind the menus is the distance command called with the additional argument mode=2.

Parameters that control the the identification of H-bonds are defined as

set h_bond_cutoff_center, 3.6

with ideal geometry and

set h_bond_cutoff_edge, 3.2

with minimally acceptable geometry.

These settings can be changed *before* running the detection process (dist
command mode=2 or via the menus).

Note that the hydrogen bond geometric criteria used in PyMOL was designed to
emulate that used by DSSP.

Hydrogen bonds between specific atoms

dist name, sele1, sele2, mode=2

Hydrogen bonds where find->polar contacts doesn't do what you need

You can show H-bonds between two objects using atom selections so long as hydrogens are present in both molecules. If you don't have hydrogens, you can use h_add on the proteins, or provide ligands with valence information and then use h_add.

Two examples are below. For clarity, they draw dashes between the heavy atoms and hide the hydrogens.

The "polar contacts" mentioned above are probably better at finding hydrogen bonds than these scripts. "Polar contacts" check geometry as well as distance.

Details

Generally speaking, PyMOL does not have sufficient information to rigorously determine hydrogen bonds, since typical PDB file are ambiguous with respect to charge states, bonds, bond valences, and tautomers. As it stands, all of those things are guessed heuristically. Rigorously determining the location of lone pair electrons and proton coordinates from raw PDB files is a nontrival problem especially when arbitrary small molecule structures are present. In addition, PyMOL would also need to consider the implied coordinate error due to overall structure resolution and local temperature factors before rigorously asserting than any specific hydrogen bond does or does not exist.

Furthermore, our hydrogen bond detection machinery was originally developed for purposes of mimicking Kabsch and Sander's DSSP secondary structure assignment algorithm (Biopolymers 22, 2577, 1983) which is based on a rather generous notion of hydrogen bonding (see Kabsch Figure 1).

Although this approximate capability can be accessed via the distance command using mode=2, the criteria applied by our implementation may be based on heavy-atom coordinates (only) and does not necessarily correspond to anything rigorous or published. So the bottom line is that PyMOL merely offers up putative polar contacts and leaves it to the user to determine whether or not the interactions present are in fact hydrogen bonds, salt bridges, polar interactions, or merely artifacts of incorrect assignments (i.e. two carbonyls hydrogen bonding because they're being treated like hydroxyls).

With respect to the h_bond_* settings, the angle in question for h_bond_cutoff_* and h_bond_max_angle is ADH, assuming H exists. If H does not exist, then PyMOL will guess a hypothetical coordinate which may not actually be valid (in plane, etc.). Tthe hydrogen must also lie within a cone of space with its origin on A (along B->A) and angular width h_bond_cone. Since h_bond_cone in 180 by default, the present behavior is to simply reject any hydrogen bond where the hydrogen would lie behind the plane defined by the acceptor atom (A) in relation to its bonded atom(s) B (if any). In other words, if B is only one atom (e.g. C=O vs. C-O-C), then by default, HAB cannot be less then 90 degrees.

The two h_bond_power_* settings are merely fitting parameters which enable PyMOL to reproduce a curve shape reflecting Kabsch Figure 1. The endpoints of the effective cutoff curve is a function of the two h_bond_cutoff_* setting.

Calculating dihedral angles

The get_dihedral function requires four single-atom selections to work:

Showing dots isn't mandatory, but it's a good idea to confirm that you're getting the value for the atom dot surface you think you're using.
Please realize that the resulting numbers are only approximate, reflecting the sum of partial surface areas for all the dots you see. To increase accuracy, set dot_density to 4, but be prepared to wait...

Display solvent accessible surface

Using the surface display mode, PyMOL doesn't show the solvent accessible surface, rather it shows the solvent/protein contact surface. The solvent accessible surface area is usually defined as the surface traced out by the center of a water sphere, having a radius of about 1.4 angstroms, rolled over the protein atoms. The contact surface is the surface traced out by the vdw surfaces of the water atoms when in contact with the protein.

PyMOL can show solvent accessible surfaces using the dot or sphere representations:

for dots:

show dots
set dot_mode,1set dot_density,3

for spheres:

alter all,vdw=vdw+1.4
show spheres

Once the Van der Waals radii for the selection have been altered, the surface representation will also be "probe-inflated" to show a pseudo solvent accessible surface, as detailed above.

for surfaces:

alter all,vdw=vdw+1.4
show surface

Solvent-Accessible Surface Example

Note that to display both the molecular surface and the solvent-accessible surface, the object must be duplicated, as is done for Surface#Representation-independent Color Control. This also applies if the spheres representation is to be used to display "real" atoms.

By displaying the protein as non-transparent surface, only the functional groups (colored atoms) at the surface are visible. The visualization of those groups can be pronounced by displaying the corresponding atoms as spheres, e.g. "as spheres, carboxy + amine_lys + sulf_cys", in this way it might become more clear how accessible they are.

When displaying the protein as cartoon, the functional groups can be shown as spheres, and the whole residues cys, lys, asp and glu as sticks connected to the backbone, with the atoms of the functional groups again as spheres. However, then also the not accessible residues inside the protein are visible.

Backbones

Displaying the C-Alpha trace of proteins

hide
show ribbon
set ribbon_sampling,1

And if your model only contains CA atoms, you'll also need to issue:

set ribbon_trace,1

Displaying the Amino Acid Backbone

The easiest way to see the backbone of the protein is to do

hide all
show ribbon

If you don't like the ribbon representation, you can also do something like

hide all
show sticks, name C+O+N+CA

You can replace sticks in the above by other representations like spheres or lines.

Displaying the Phosphate backbone of nucleic acids

Native Nucleic Acid Rendering in PyMol

PyMol now better supports viewing nucleic acid structure. Nuccyl still seems to be the reigning champ for image quality, but see PyMol's native Cartoon command. For more information on representing nucleic acids, please see the Nucleic Acids Category.

Should you ever want to show the phosphate trace of a nucleic acid molecule:

Align proteins with CA fit

If two proteins have significant homology, you can use the Align command:

align prot1////ca,prot2

which will perform a sequence alignment of prot1 against prot2, and then an optimizing fit using the CA positions. I'm not sure if the help text for align got into 0.82, but the next version will definitely have it.